Mesh modeling review: black hole, cannot select face, joining subdivisions
Your question is loaded with many questions that appear to be regarding best modeling practices.
Quads vs N-Gons
In general, there are many ways to model something with either quad or n-gons. You have to ask yourself what you would like your end result to be.

For example, if you are modeling something that you wish you use a subdivision modifier or use loop cuts, then it is best practice to use quads.
If you are modeling a low poly asset that you wish to export to a game engine, then it is also preferable to use quads (that will then get triangulated upon export).
If you are modeling something that you wish to render within Blender as is, without the need to subdivide the geometry further, then n-gons are suitable to use as well.

In your case, since the hulls of boats are usually smooth, you may need to add additional loops and/or use subdivision modifier, so it is recommended to use quads.
Normals direction
Your next question is regarding the direction of your normals. If their are pointing inwards, then they appear dark.

to enable viewing normals, open up the &quot;N&quot; toolbar by pressing the N key on your keyboard in edit mode, and scroll down to select &quot;view face normals&quot;
You can flip the normal of a face by selecting it, and searching for the flip normals command (using the space bar).


Limiting Selection to visible
Based on the file you provided, you cannot select the face at the bottom of the cockpit because you had you have not limited your selection to visible, meaning you can see the bottom faces in solid view.
To enable the option, click the &quot;limit selection to visible&quot; button in the 3d viewport header
Joined vs separate objects

Similarly to the consideration required for quads vs n-gons, it's best to think about what is the required end result.
If some smootheness (via subdivision modifier or additional edge loops), then it's best to have connected objects. However, they should also be quads.
It instead you are modeling disparate elements, then there is no need for the meshes to share vertices.


Best modeling practices
In general with mesh modeling, it is better to start from a single object that you can then subdivide with loop cuts and/or extrusions to get the desired result. I would suggest going through tutorials on youtube.
Below is a quick example of how to model the boat starting from a plane, with a few edge loops, extruding, adding subdivision modifier, and adding additional edge loops to control the softness/hardness of edges.